DNA Based Computing
Published on Feb 21, 2020
Biology is now the study of information stored in DNA - strings of four letters: A, T, G, and C for the bases adenine, thymine, guanine and cytosine - and of the transformations that information undergoes in the cell. There were mathematics here?
DNA polymerase is the king of enzymes - the maker of life. Under appropriate conditions, given a strand of DNA, DNA polymerase produces a second "Watson-Crick" complementary strand, in which every C is replaced by a G, every G by a C, every A by a T and every T by an A.
For example, given a molecule with the sequence CATGTC, DNA polymerase will produce a new molecule with the sequence GTACAG. The polymerase enables DNA to reproduce, which in turn allows cells to reproduce and ultimately allows you to reproduce. For a strict reductionist, the replication of DNA polymerase is what life is is all about.
DNA polymerase is an amazing little nanomachine, a single molecule that "hops" onto a strand of DNA and slides along it, "reading " each base it passes and "writing" its complement onto a new, growing DNA strand. This was in similarity to the Turing machine (toy computer) suitable for mathematical investigation on the study of the notion of "computability" which preceded the advent of actual computers by about a decade and led to some of the major mathematical results of the 20th century.
The most striking was that Turing's toy computer had turned out to be universal and could be programmed to compute anything that was computable at all. In other words, one could programme a Turing machine to produce Watson-Crick complementary strings, factor numbers, play chess and so on.
To build a DNA computer, tools were essential such as (1) Watson-Crick pairing (2) polymerases (3) Ligases (4) Nucleases (5)Gel electrophoresis, and (6) DNA synthesis.
To build a computer, only two things are really necessary - a method of sorting information and a few simple operations for acting on that information.
DNA Computer Building
The Unrestricted model of DNA computing:
To build a DNA computer, the tools were essentially the following -
1. Watson-Crick pairing - every strand of DNA has its Watson-Crick complement.
2. Polymerases - to copy information from one molecule into another.
3. Ligases - to bind molecules together.
4. Nucleases -to cut nucleic acids.
5. Gel electrophoresis - a process to separate DNA by length
6. DNA synthesis - to write a DNA sequence on a piece of paper.
Since Adleman's original experiment, several methods to reduce error and improve efficiency have been developed. The Restricted model of DNA computing solves several physical problems with the Unrestricted model. The Restricted model simplifies the physical obstructions in exchange for some additional logical considerations. The purpose of this restructuring is to simplify biochemical operations and reduce the errors due to physical obstruction